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Old 11-24-2014, 03:59 AM   #1
Location: India

Join Date: Jun 2013
Posts: 14
Default Finding contaminant contigs in assembly


I have generated plant mitochondrial assembly for which I would like to find contamination from chloroplast as well as nuclear genome. I have also run BlastN using same species nuclear genome and chloroplast genome database, and now with results I have some alignments with multiple scaffolds generated.

My question is, if it is wise cutting down sequences from assembly which are having high identity with substantive e-value with subject sequences or I need to see some other criteria along with identity and e-value?

Any help would be highly appreciated...
mandar.bobade60 is offline   Reply With Quote
Old 12-04-2014, 03:31 AM   #2
Location: Germany/Netherlands

Join Date: Feb 2014
Posts: 98

What about the length?
Longer alignment > smaller one.
bastianwur is offline   Reply With Quote

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